Mass Spectroscopy
description
Transcript of Mass Spectroscopy
![Page 1: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/1.jpg)
Mass Spectroscopy
Alireza Ghassempour (PhD)
Medicinal Plants and Drugs Research InstituteShahid Beheshti University
Evin, Tehran
![Page 2: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/2.jpg)
Operational sequenceOperational sequence
introduce introduce samplesample ionizeionize separate by separate by
mass/chargemass/chargedetect ionsdetect ions
![Page 3: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/3.jpg)
Sample introductionSample introduction
![Page 4: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/4.jpg)
Ionization methodsIonization methods
EI – direct interaction of electrons with sampleEI – direct interaction of electrons with sampleCI – electrons ionize reagent gasesCI – electrons ionize reagent gasesDI – uses a pulse of energy to produce ionsDI – uses a pulse of energy to produce ionsSI – converts solvated molecules into ionsSI – converts solvated molecules into ions
![Page 5: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/5.jpg)
![Page 6: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/6.jpg)
![Page 7: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/7.jpg)
electron ionizationelectron ionization
There will be different degrees of fragmentation There will be different degrees of fragmentation depending on the stability of the sample moleculedepending on the stability of the sample molecule
For a stable aromatic compound the primary peak is the parent ionFor a stable aromatic compound the primary peak is the parent ionFor a less stable cyclic compound fragmentation is predominantFor a less stable cyclic compound fragmentation is predominant
![Page 8: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/8.jpg)
Chemical ionizationChemical ionization
Chemical ionization is a more controlled method Chemical ionization is a more controlled method of ionization than electron ionizationof ionization than electron ionization
In CI a neutral analyte (M) reacts with a reagent In CI a neutral analyte (M) reacts with a reagent ion that is generated by EI to form a variety of ion that is generated by EI to form a variety of molecular ionsmolecular ions
**
![Page 9: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/9.jpg)
![Page 10: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/10.jpg)
Desorption ionizationDesorption ionization
1.1. Energetic primary ions Energetic primary ions secondary ion mass spectrometry (SIMS)secondary ion mass spectrometry (SIMS)
2.2. Energetic atoms Energetic atoms fast atom bombardment (FAB)fast atom bombardment (FAB)
3.3. Nuclear fission fragments Nuclear fission fragments plasma desorption (PD)plasma desorption (PD)
4.4. Photons Photons laser desorption (LD)laser desorption (LD)
5.5. Very rapid heatingVery rapid heatingdesorption chemical ionization (DCI)desorption chemical ionization (DCI)
![Page 11: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/11.jpg)
FAB ionization matricesFAB ionization matrices
Optimal matrix propertiesOptimal matrix propertiesStrongly absorbs the energy providedStrongly absorbs the energy provided
Contributes few ions to the spectrumContributes few ions to the spectrum
Interacts with the analyte to produce ionsInteracts with the analyte to produce ions
Effectively transfers energy to the analyte ionsEffectively transfers energy to the analyte ions
![Page 12: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/12.jpg)
Diagram of an FAB gun. 1, Ionization of argon; the resultingions are accelerated and focused by the lenses 2. In 3, the argon ions exchange their charge with neutral atoms, thus becoming rapid neutral atoms. As the beam path passes between the electrodes 4, all ionic species are deflected. Only rapid neutral atoms reach the sample dissolved in a drop of glycerol, 5. The ions ejected from the drop are accelerated by the pusher, 6, and focused by the electrodes, 7, towards the analyser, 8.
![Page 13: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/13.jpg)
Depending on the nature of the matrix we can obtain different molecular ionsDepending on the nature of the matrix we can obtain different molecular ions
protonated protonated speciesspecies
deprotonated deprotonated speciesspecies
Ag saltAg salt
Why are there two peaks?107Ag and 109Ag
![Page 14: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/14.jpg)
Spray ionization methodsSpray ionization methods
Spray ionization achieves the direct conversion of non-volatile, Spray ionization achieves the direct conversion of non-volatile, solvated molecules into gas phase ionssolvated molecules into gas phase ions
![Page 15: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/15.jpg)
Electrospray (ESI)
![Page 16: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/16.jpg)
Electrospray ionizationElectrospray ionization
ESI-MS of cytochrome c (mw = 12,360)
The isotope distribution also allows charge assignment, since each The isotope distribution also allows charge assignment, since each isotopic peak is separated from the next by 1/n where n is the chargeisotopic peak is separated from the next by 1/n where n is the charge
peak separation is 1/15peak separation is 1/15
![Page 17: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/17.jpg)
Principles of MALDI The sample is dispersed in a large excess of matrix material which will
strongly absorb the incident light. The matrix contains chromophore for the laser light and since the matrix
is in a large molar excess it will absorb essentially all of the laser radiation
The matrix isolates sample molecules in a chemical environment which enhances the probability of ionization without fragmentation
Short pulses of laser light (UV, 337 nm) focused on to the sample spot cause the sample and matrix to volatilize
The ions formed are accelerated by a high voltage supply and then allowed to drift down a flight tube where they separate according to mass
Arrival at the end of the flight tube is detected and recorded by a high speed recording device
![Page 18: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/18.jpg)
Matrix Assisted Laser Desorption
![Page 19: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/19.jpg)
MatricesMatrix
1,8,9-Trihydroxyanthracen(Dithranol) polymers
2,5-Dihydroxybenzoicacid(DHB)
proteins,peptides,polymers
-Cyano-4-hydroxycinnamicacid
peptides,(polymers)
4-Hydroxypicolinicacid oligonucleotides
Trans-Indol-3-acrylacid(IAA)
polymers
OH OH OH
OH
OH
COOH
C CH
OH
CN COOH
N
OH
COOH
NH
COOH
![Page 20: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/20.jpg)
Sample Preparation: Dried Droplet
solvedMatrix solvedsample
MixingandDrying
![Page 21: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/21.jpg)
Sample Preparation: Thin Layer
solvedMatrix
solvedsample
fastdrying
thin homogenuouslayer of crytslas
Drying
![Page 22: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/22.jpg)
MALDI spectra of a monoclonal antibody (above) and of a polymer PMMA 7100 (below).
![Page 23: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/23.jpg)
Secondary Ion Mass Spectrometry (SIMS)
![Page 24: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/24.jpg)
Secondary ion generation
The sample is prepared in an ultra high vacuum.
A beam of primary ions or neutral particles impacts the surface with energies of 3-20 keV.
A primary ion or particle causes a collision cascade amongst surface atoms and between .1 and 10 atoms are usually ejected. This process is termed sputtering. The sputter yield depends on the nature of the analyte.
![Page 25: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/25.jpg)
Static SIMS Low ion flux is used. This means a small amount of
primary ions is used to bombard the sample per area per unit time. Sputters away approximately only a tenth of an atomic monolayer.
Ar+, Xe+, Ar, and Xe are the commonly used particles present in the primary particle beam, which has a diameter of 2-3 mm.
The analysis typically requires more than 15 minutes. This technique generates mass spectra data well
suited for the detection of organic molecules.
![Page 26: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/26.jpg)
Imaging SIMS The mass spectrometer is set
to only detect one mass. The particle beam traces a
raster pattern over the sample with a low ion flux beam, much like Static SIMS.
Typical beam particles consists of Ga+ or In+ and the beam diameter is approximately 100 nm.
The analysis takes usually less than 15 min. The intensity of the signal detected for the particular mass is
plotted against the location that generated this signal. Absolute quantity is difficult to measure, but for a relatively
homogeneous sample, the relative concentration differences are measurable and evident on an image.
Images or maps of both elements and organics can be generated.
![Page 27: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/27.jpg)
Images created using the Imaging SIMS mode.
Scanning ion image of granite from the Isle of Skye.-University of Arizona SIMS 75 x 100 micrometers.
![Page 28: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/28.jpg)
Mass Analyzers
![Page 29: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/29.jpg)
Mass Analyzer divided into:1. Scanning analysers transmit:1.1 only the ions of a given mass-to-chargeratio to go through at a given time (magnetic, qudrupole)1.2. allow the simultaneous transmission of all ions (ion trap, TOF)
2. ion beam versus ion trapping types, 3. continuous versus pulsed analysis, 4. low versus high kinetic energies
![Page 30: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/30.jpg)
The five main characteristics for mass analyser:1. The mass range limit (Th) 2. The analysis speed (u s−1) 3. The transmission (the ratio of the number of ions reaching
the detector and the number of ions entering the mass analyser, a quadrupole MS used in SIM mode has a duty cycle of 100 % but a quadrupole MS scanning over 1000 amu, the duty cycle is
1/1000=0.1%. )4. The mass accuracy (ppm)5. The resolution.
![Page 31: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/31.jpg)
Two peaks are considered to be resolved if the valley between them is equal to 10% of the weaker peak intensity when using magnetic or ion cyclotron resonance (ICR) instruments and 50% when using quadrupoles, ion trap, TOF, and so on.
R=m/∆m
Low resolution or high resolution is usually used to describe analysers with a resolving power that is less or greater than about 10 000 (FWHM), respectively
![Page 32: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/32.jpg)
The first example is human insulin, a protein having the molecular formula C257H383N65O77S6.
The nominal mass of insulin is 5801 u using the integer mass of the most abundant isotope of each element, such as 12 u for carbon, 1u for hydrogen, 14 u for nitrogen, 16 u for oxygen and 32 u for sulfur.
Its monoisotopic mass of 5803.6375 u is calculated using the exact masses of the predominant isotope of each element such as C=12.0000 u, H=1.0079 u, N=14.0031 u, O=15.9949 u and S=31.9721 u.
![Page 33: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/33.jpg)
Monoisotopic mass / Average Mass
Monoisotopic mass
Average mass
![Page 34: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/34.jpg)
![Page 35: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/35.jpg)
Magnetic-Sector
THEORY:
The ion source accelerates ions to a kinetic energy given by:
KE = ½ mv2 = qV
Where m is the mass of the ion, v is its velocity, q is the charge on the ion, and V is the applied voltage of the ion optics.
![Page 36: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/36.jpg)
Magnetic-Sector
•The ions enter the flight tube and are deflected by the magnetic field, B.
•Only ions of mass-to-charge ratio that have equal centripetal and centrifugal forces pass through the flight tube:
mv2 /r = BqV, where r is the radius of curvature
![Page 37: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/37.jpg)
Magnetic-Sector
mv2 /r = BqV
•By rearranging the equation and eliminating the velocity term using the previous equations, r = mv/qB = 1/B(2Vm/q)1/2
•Therefore, m/q = B2r2/(2V)
•This equation shows that the m/q ratio of the ions that reach the detector can be varied by changing either the magnetic field (B) or the applied voltage of the ion optics (V).
![Page 38: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/38.jpg)
Basis of Quadrupole Mass Filter
consists of 4 parallel metal rods, or electrodes
opposite electrodes have potentials of the same sign
one set of opposite electrodes has applied potential of [U+Vcos(ωt)]
other set has potential of - [U+Vcosωt] U= DC voltage, V=AC voltage,
ω= angular velocity of alternating voltage
![Page 39: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/39.jpg)
The trajectory of an ion will be stable if the values of x and y never reach r0, thus if it never hits the rods. To obtain the values of either x or y during the time, these equations need to be integrated. The following equation was established in 1866 by the physicist Mathieu :
![Page 40: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/40.jpg)
Mass analyzersMass analyzers
An ion trap is a device that uses an oscillating electric field to store ions. The ion trap works by using an RF quadrupolar field that traps ions in two or three dimensions (2D and 3D).
![Page 41: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/41.jpg)
Ion Trap MS Ions are trapped by applying
rf frequencies on the ring electrode and endcaps
Then ions are scanned out of the trap by m/z as the base mass voltage is increased over time
This is accomplished by maintaining in the trap a pressure of helium gas which removes excess energy from the ions by collision.
![Page 42: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/42.jpg)
• The Back Plate and Grid are used to accelerate the ions• The Ion source is used to ionize the Sample
• The Sample Inlet introduces the sample to the source• The vacuum is used to maintain a low pressure
• The Drift Region separates the ions according to their mass• The Detector outputs current as each ion strikes it
• The Oscilloscope displays the detector output
Time of Flight Schematic
![Page 43: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/43.jpg)
Time-of-Flight Converted to Mass An accelerating potential (V) will give an ion of charge z an energy of zV. This can be
equated to the kinetic energy of motion and the mass (m) and the velocity (v) of the ion
zV = 1/2mv2
Since velocity is length (L) divided by time (t) then
m/Z = [2Vt2]/L2
V and L cannot be measured with sufficient accuracy but the equation can be rewritten
m/Z = B(t-A)2
where A and B are calibration constants that can be determined by calibrating to a known m/Z
![Page 44: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/44.jpg)
Reflectron TOF-MS Improved mass resolution in MALDI TOF-MS has been obtained by the utilization of a single-stage or a dual-stage reflectron (RETOF-MS). The reflectron, located at the end of the flight tube, is used to compensate for the difference in flight times of the same m/z ions of slightly different kinetic energies by means of an ion reflector. This results in focusing the ion packets in space and time at the detector
![Page 45: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/45.jpg)
A typical MALDI mass spectrum of substance P in CHCA (see Table 1) employing both linear and reflectron TOF-MS in the continuous ion extraction mode with a 500 MS/s transient digitizer is shown. The maximum mass resolution observed in the linear mass spectrum of substance P employing continuous ion extraction is about 600 which is typical for a peptide of this size. Only the average chemical mass can be determined from this mass spectrum. In the reflectron mass spectrum, the isotopic multiplet is well resolved producing a full width half maximum (FWHM) mass resolution of about 3400
![Page 46: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/46.jpg)
FT-ICR-MS instrument general scheme
![Page 47: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/47.jpg)
FTICR: New Dimensions of High Performance Mass Spectrometry
Ionsaretrappedandoscillatewithlow,incoherent,thermalamplitudeExcitationsweepsresonantionsintoalarge,coherentcyclotronorbitPreamplifieranddigitizerpickuptheinducedpotentialsonthecell.
![Page 48: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/48.jpg)
FTICR: New Dimensions of High Performance Mass Spectrometry
Thefrequencyofthecyclotrongyrationofanionisinverselyproportionaltoitsmass-to-chargeratio(m/q)anddirectlyproportionaltothestrengthoftheappliedmagneticfieldB.
![Page 49: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/49.jpg)
B
v
BvqFL
+
Excitationelectrodes
Detection electrodes
Fourier Transform Ion Cyclotron Resonance Mass Spectrometry
+
-100
-80
-60
-40
-20
0
20
40
60
80
100
Inte
nsity
[%]
Time
ExciteDetect77 - Frequency spectrumWideband (BW: 500.000k) accumulated 5 scans
Frequency [Hz] x1E350 60 70 80 90 100 110 120 130 140 150 160 170
Inte
nsity
[%]
0
20
40
60
80
100
Frequency
Fourier Transform
Time
0
Inte
nsity
[%
]
mqBf2
0
MS spec with only one frequency
Fourier Transform
![Page 50: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/50.jpg)
ExciteDetect77 - Magnitude spectrumWideband (BW: 500.000k) serial scan 21 of 50
874.87
874.94
875.01
875.08
875.15875.22
875.29875.36
875.43
875.50
875.58
875.65875.72
Masses [m/z]874.8 874.9 875 875.1 875.2 875.3 875.4 875.5 875.6 875.7 875.8
Inte
nsity
[%]
0
10
20
30
40
50
60
70
80
90
100
110
High Resolution of FTICR MS
Ubiquitin (14+)
Mass resolution: 170,000
(up to 5,000,000)
mass
![Page 51: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/51.jpg)
Finnigan LTQ FT Ultra
51
![Page 52: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/52.jpg)
Finnigan LTQ FT Ultra
52
![Page 53: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/53.jpg)
Biological samplesCeribrospinal fluid (CSF), 1µL Injection volume200 nL/min, Nanospray, D:\Data\...\HUPO\CSF79_120-30_SIM_LC154 18.08.2005 06:06:46
RT: 0.00 - 150.00
0 10 20 30 40 50 60 70 80 90 100 110 120 130 140Time (min)
0
10
20
30
40
50
60
70
80
90
100
Rel
ativ
e A
bund
ance
95.17
56.02
80.5469.62104.4856.58
20.47 80.90141.4170.0750.39 86.3922.48
96.9290.5338.31 143.1873.74
26.79 110.7665.7435.99 114.5744.45 130.52117.43 134.06123.0620.11 33.35
18.4814.289.68
NL:2.70E8TIC F: MS CSF79_120-30_SIM_LC154
CSF79_120-30_SIM_LC154 #7925 RT: 49.57 AV: 1 NL: 1.40E6T: FTMS + p NSI Full ms [ 300.00-2000.00]
400 600 800 1000 1200m/z
0
10
20
30
40
50
60
70
80
90
100
Rel
ativ
e A
bund
ance
660.91
499.75
551.09
451.27
825.89
702.55613.77
435.77330.46
850.90737.35 936.72 1207.85319.86 1080.97
CSF79_120-30_SIM_LC154 #7929 RT: 49.60 AV: 1 NL: 2.01E5T: ITMS + c NSI d Full ms2 [email protected] [ 170.00-2000.00]
200 400 600 800 1000 1200 1400m/z
0
10
20
30
40
50
60
70
80
90
100
Rel
ativ
e A
bund
ance
838.67
394.99
767.20
542.31743.35 1028.77458.38 1138.85337.49
876.52 1396.211214.29
MS Peptide mass MS/MS Peptide sequence
TIC Separation of peptides
660.91
m/z m/z
Retention Time, min
![Page 54: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/54.jpg)
Finnigan LTQ FT Ultra – MS/MS
54
![Page 55: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/55.jpg)
Biological samplesCeribrospinal fluid (CSF), 1µL Injection volume200 nL/min, Nanospray, D:\Data\...\HUPO\CSF79_120-30_SIM_LC154 18.08.2005 06:06:46
RT: 0.00 - 150.00
0 10 20 30 40 50 60 70 80 90 100 110 120 130 140Time (min)
0
10
20
30
40
50
60
70
80
90
100
Rel
ativ
e A
bund
ance
95.17
56.02
80.5469.62104.4856.58
20.47 80.90141.4170.0750.39 86.3922.48
96.9290.5338.31 143.1873.74
26.79 110.7665.7435.99 114.5744.45 130.52117.43 134.06123.0620.11 33.35
18.4814.289.68
NL:2.70E8TIC F: MS CSF79_120-30_SIM_LC154
CSF79_120-30_SIM_LC154 #7925 RT: 49.57 AV: 1 NL: 1.40E6T: FTMS + p NSI Full ms [ 300.00-2000.00]
400 600 800 1000 1200m/z
0
10
20
30
40
50
60
70
80
90
100
Rel
ativ
e A
bund
ance
660.91
499.75
551.09
451.27
825.89
702.55613.77
435.77330.46
850.90737.35 936.72 1207.85319.86 1080.97
CSF79_120-30_SIM_LC154 #7929 RT: 49.60 AV: 1 NL: 2.01E5T: ITMS + c NSI d Full ms2 [email protected] [ 170.00-2000.00]
200 400 600 800 1000 1200 1400m/z
0
10
20
30
40
50
60
70
80
90
100
Rel
ativ
e A
bund
ance
838.67
394.99
767.20
542.31743.35 1028.77458.38 1138.85337.49
876.52 1396.211214.29
MS Peptide mass MS/MS Peptide sequence
TIC Separation of peptides
660.91
m/z m/z
Retention Time, min
![Page 56: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/56.jpg)
LC-MS/MS
56
![Page 57: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/57.jpg)
Orbitrap- a new type of FTMS
![Page 58: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/58.jpg)
Click to edit Master title style
58
Principle of Trapping in the Orbitrap
Orbital trapsKingdon (1923)
The Orbitrap is an ion trap – but there are no RF or magnet fields!
• Moving ions are trapped around an electrode- Electrostatic attraction is compensated by centrifugal force arising from the initial tangential velocity. Analogon: a satellite is “trapped” around the Earth; a satellite is “trapped” around the Earth; gravitational attraction is compensated by centrifugal gravitational attraction is compensated by centrifugal force arising from initial tangential velocity.force arising from initial tangential velocity.
• Potential barriers created by end-electrodes confine the ions axially
• The frequencies of oscillations (especially the axial ones) could be controlled by shaping the electrodes appropriately
• Thus we arrive at …
![Page 59: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/59.jpg)
LTQ Orbitrap™ Hybrid Mass SpectrometerLaunched in Summer 2005
API Ion source Linear Ion Trap C-Trap
Orbitrap
Finnigan LTQ™ Linear Ion Trap
Differential pumping
Differential pumping
Inventor: Dr. Alexander Makarov, Thermo Fisher Scientific (Bremen, Germany)
![Page 60: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/60.jpg)
LTQ Orbitrap Operation Principle1. Ions are stored in the Linear Trap2. …. are axially ejected3. …. and trapped in the C-trap4. …. they are squeezed into a small cloud and injected into the Orbitrap5. …. where they are electrostatically trapped, while rotating around the central electrode and performing axial oscillation
The oscillating ions induce an image current into the two outer halves of the Orbitrap, which can be detected using a differential amplifier
Ions of only one mass generate a sine wave signal
![Page 61: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/61.jpg)
The axial oscillation frequency follows the formula Where = oscillation frequency
k = instrumental constant m/z = …. well, we have seen this before
zmk/
Frequencies and Masses
Many ions in the Orbitrap generate a complex signal whose frequencies are determined using a Fourier Transformation
![Page 62: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/62.jpg)
What‘s the size of the Orbitrap?
![Page 63: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/63.jpg)
LTQ Orbitrap™ Hybrid Mass Spectrometer
![Page 64: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/64.jpg)
Tandem mass spectrometersTandem mass spectrometers
Uses of tandem mass spectrometry:Uses of tandem mass spectrometry:
(1)(1) Characterize individual compounds in complex mixturesCharacterize individual compounds in complex mixtures
(2)(2) Completely identify the molecular structure of a compoundCompletely identify the molecular structure of a compound
To accomplish either of these goals mass analysis To accomplish either of these goals mass analysis must be carried out twice in a tandem instrumentmust be carried out twice in a tandem instrument
This can be achieved either by separating the This can be achieved either by separating the mass analysis operations in space or in timemass analysis operations in space or in time
![Page 65: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/65.jpg)
Tandem mass spectrometersTandem mass spectrometers
![Page 66: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/66.jpg)
Information obtained from MS experimentsChemical Ionization
(CI)
Electron impact Ionization(EI)
GC-MS LC-MS
-TOF Product (185.0): 1.750 to 3.300 min from pinic_P185.wiffa=3.56215314471457500e-004, t0=4.61223072761931690e+001
Max. 46.2 counts.
115 120 125 130 135 140 145 150 155 160 165 170 175 180 185 190 195m/z, amu
0
5
10
15
20
25
30
35
40
45
Inte
ns
ity, c
ou
nts
141.09268
185.08193123.08251 167.07195
-TOF Product (185.1): 1.267 to 2.317 min from Sample 5 (ESI-: pinic P185 CE=-6, CAD=2) of 0...a=3.56228408459780370e-004, t0=4.72207389233553840e+001
Max. 170.6 counts.
40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190m/z, amu
0
10
20
30
40
50
60
70
80
90
100
110
120
130
140
150
160
170
Inte
ns
ity, c
ou
nts
185
COOH
COOH
MS
MS/MS
Molecular weight
Structural information
![Page 67: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/67.jpg)
Separation in space can be achieved by coupling two mass analyzersSeparation in space can be achieved by coupling two mass analyzers
For example, a sector magnet (MS 1) can be coupled to a For example, a sector magnet (MS 1) can be coupled to a quadrupole mass filter (MS 2)quadrupole mass filter (MS 2)A parent ion is selected by the sector magnet and A parent ion is selected by the sector magnet and separated from the other ions in the sampleseparated from the other ions in the sampleEach selected ion is activated by a collision processEach selected ion is activated by a collision processThe resulting set of product ions are analyzed by the The resulting set of product ions are analyzed by the quadrupole mass filterquadrupole mass filter
![Page 68: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/68.jpg)
Tandem mass spectrometersTandem mass spectrometersThe most common tandem mass spectrometer The most common tandem mass spectrometer
is a triple quadrupole mass spectrometeris a triple quadrupole mass spectrometer
![Page 69: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/69.jpg)
Mass Spec Ion Detectors
Faraday Cup Electron Multiplier and Channel Electron
Multiplier Microchannel Plate Daly Detector (Scintillation Counter or
Photomultiplier)
![Page 70: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/70.jpg)
Electron Multipliers
![Page 71: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/71.jpg)
Continuous Electron Multiplier
![Page 72: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/72.jpg)
Photomultiplier (Daly detector)
![Page 73: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/73.jpg)
Photomultiplier
Also called daly detector or scintillation counter Metal dynode emits secondary electrons Secondary electrons hit phosphorus screen and
trigger photon emission; photon abundance measured by photomultiplier
Advantage: keep detector in vacuum -- no contamination = low noise and long lifetime
Disadvantage: cannot be exposed to light
![Page 74: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/74.jpg)
Data Collection
Typically, the computer controls: Scanning of mass spec Data acquisition Data processing Interpretation of data (generation of spectra;
possible comparison to spectra in database)
![Page 75: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/75.jpg)
Sequencing Using MALDIWhen the molecular mass of a peptide is known, for example Gly2Tyr = 296, we may use a digested, or fragmented effect of MALDI to learn the sequence of the peptide. Backbone (peptide bond) cleavages in the mass spectrometer generate two types of ions. Acylium ions are produced when the charge is retained on the N-terminal side of the peptide, while protonated peptides are produced when the charge is retained on the C-terminal side of the peptide. These ion fragments are known as bn and yn fragments respectively. In straightforward cases, all possible fragments are produced using prior peptide digestion. This means that for a given peptide sequence, two unique sets of fragment ions are produced (the bn and yn sets). In the following table, the “predicted” fragments for a given peptide are listed. Comparison of these predicted fragments with experimentally observed peptide fragments allows for a given peptide mass to be assigned to a unique peptide sequence.
![Page 76: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/76.jpg)
Formulas for prediction of mass spectrometer fragments during the analysis of peptides.
Two series (bn and yn) are produced, depending on the peptide end on which cleavage occurs
b1 Mresidue + H y1 Mresidue + 19
b2 Mresidue + b1 y2 Mresidue + y1
bn-1 MH+ - 18 - Mresidue Yn-1 MH+ - Mresidue
![Page 77: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/77.jpg)
ExampleConsider the peptide GlyTyr. Two possible sequences are possible:
H-Gly-Tyr-OH H-Tyr-Gly-OH
The predicted fragments for these two sequences would be:
H-Tyr-Gly-OH H-Gly-Tyr-OH
b1 = 164 b1 = 58
b2 = 221 b2 = 221
y1 = 76 y1 = 182
y2 = 239 y2 = 239
Suppose experimentally, we detected fragments at mass 164, 221 but none at 239. This missing mass is sufficient to identify the sequence as H-Tyr-Gly-OH.
![Page 78: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/78.jpg)
Peptide Fingerprinting
MALDI may be used to determine an exact “peptide fingerprint” of a section of a protein that carries a “disease” or differs from the normal protein in some way.
![Page 79: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/79.jpg)
C-1
C-2
C -3
Tox-1
Tox-2
Tox-3
Standard Control 2D Gel
Results: 196 features detected; 40 ( ) at 2-fold change.
Digitized Image
Digitized PDQuest image following matchset comparison, which allows comparison of all control versus all toxicant images. Each black spot represents a protein; spots circled in yellow indicate prot. eins with at least a 2-fold change based on spot intensity or statistical test
Image Analysis for Differential Protein Expression
![Page 80: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/80.jpg)
Protein Identification by MALDI-MS• Differentially expressed proteins identified by image analysis are excised from 2D gels and trypsin digested. The resulting peptide fragments are analyzed on a MALDI mass spectrometer (MS).
• The MALDI spectra displays a “peptide fingerprint” of the protein using corresponding peptide masses.
![Page 81: Mass Spectroscopy](https://reader031.fdocuments.in/reader031/viewer/2022013012/56815ce2550346895dcae535/html5/thumbnails/81.jpg)
Database Searching using MALDI-MS Ions for Protein Identification
• Proteins are identified by entering the masses (ions from MALDI spectrum) of the peptides into a peptide mapping database such as ProFound.
• Search parameters are refined by including experimental mass and isoelectric point (pI) determined by 2D PAGE, as well as by taxonomic category and any modifications.
http://prowl.rockefeller.edu/cgi-bin/ProFound